Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Merged in barry/optimize-aij-da (pull request #1762)

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some Pets

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some PetscMalloc*()
3) Eliminated unneeded PetscCalloc*()
4) Removed some memory allocations and copies in MatFDColoringSetUp(), added local variables for better compiler optimization
5) Added MatSetValues_SeqAIJ_SortedFull(), added MatSetOption(MAT_SORTED_FULL)
6) Optimized DMCreateMatrix_DA_*AIJ for nonperiodic case to automatically have sorted columns (faster MatSetValues() times)
7) Eliminated call to PetscMemzero() in PetscFree()

Commit-type: style-fix, feature

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Merged in jed/makefile.user (pull request #1683)

Add Makefile.user, which uses pkg-config

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Satish Balay <balay@mcs.anl.gov>

PetscViewerHDF5Load: move to isimpl.h and make INTERN

This function does not have a man page and depends on H5Ipublic.h, which
should not be requried for users who don't intend to call HDF5.

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge remote-tracking branch 'origin/maint'

Merged in haplav/fix-hdf5v-circular-dependencies (pull request #1643)

fix hdf5v circular dependencies

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Merged in haplav/fix-hdf5v-circular-dependencies (pull request #1643)

fix hdf5v circular dependencies

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Jed Brown <jed@59a2.org>

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Move HDF5 array IO stuff from sys to vec.

- Fix issue 288.
- Moved PetscViewerHDF5Load,PetscViewerHDF5ReadSizes and their helpers from
src/sys/classes/viewer/impls/hdf5/hdf5v.c
into the new fi

Move HDF5 array IO stuff from sys to vec.

- Fix issue 288.
- Moved PetscViewerHDF5Load,PetscViewerHDF5ReadSizes and their helpers from
src/sys/classes/viewer/impls/hdf5/hdf5v.c
into the new file
src/vec/is/utils/hdf5io.c
- PetscViewerHDF5Load() header moved from viewerimpl.h to petscis.h
- PetscViewerHDF5ReadSizes() header moved from petscviewerhdf5.h to petscis.h

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Merged in barry/is-need-not-include-vec (pull request #1611)

Remove unneccesary references to petscvec.h and vecimpl.h from lower level routines such as IS

Approved-by: Matthew Knepley <knepley@gma

Merged in barry/is-need-not-include-vec (pull request #1611)

Remove unneccesary references to petscvec.h and vecimpl.h from lower level routines such as IS

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: Václav Hapla <vaclav.hapla@erdw.ethz.ch>

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Remove unneccesary references to petscvec.h and vecimpl.h from lower level routines such as IS

Commit-type: style-fix
Thanks-to: Matthew Knepley <knepley@gmail.com>

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-snes-patch

Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and dom

Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and domain size for test _2."
DMStag tutorial ex4: fix stencil errors
Hierarchical partitioner: added an alt output file
Add support for DMGetMatrix() with periodic boundary conditions in one dimension for DMDA.
Fixed incorrect 'ntext' argument in PetscOptionsEList call in SNES ex12.c
ISCreateSubIS: Initialize variables owner and lidx to avoid compiler warnings
metis: provide -download-metis-use-doubleprecision option
KSP ex56: Updated test output and domain size for test _2.
Hierarchical partitioner: add a bit documentation
ISCreateSubIS: Added checkers for parameters
Added a test for hierarchical partitioning vertex weights
Plex+Doc: Document options for DMPlexCreateBoxMesh()
Hierarchical partitioner supports vertex weights
Create an API ISCreateSubIS that extracts
Add an alt output file
Plex: Can now give bounds to DMPlexCreateBoxMesh() from options - Use -dm_plex_box_lower and dm_plex_box_upper
PCMG: These methods should be optional
PCMG: Make PCMGGet/SetLevels() proper member functions - Also need to compose them in GAMG
...

Conflicts:
src/dm/impls/plex/plexsection.c

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Merge branch 'Fande-Kong/fixed_hierarchical_partitioning_weights_master'

Create an API ISCreateSubIS that extracts

part of the original IS.

This API is similar to MatCreateSubMatrix

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'haplav/feature-dmplex-check-interface-cone-conformance' [PR #1164]

* haplav/feature-dmplex-check-interface-cone-conformance:
DMPlex: check for interface cone conformance
New DMPlexChec

Merge branch 'haplav/feature-dmplex-check-interface-cone-conformance' [PR #1164]

* haplav/feature-dmplex-check-interface-cone-conformance:
DMPlex: check for interface cone conformance
New DMPlexCheckConesConformOnInterfaces() checks that cones of points on inter-partition interfaces have conforming order.
This check is now called in DMPlex test ex18.c. To reproduce the failed check, one can remove requires: TODO from tests.
This merge also adds DMGetCoordinatesLocalSetUp() and DMGetCoordinatesLocalNoncollective() as I needed a non-collective version of DMGetCoordinatesLocal(), and fixes several notes on collectiveness in DMPlex documention.

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Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master